Mark
The thick flange block is the most sought after 1275cc Midget/Sprite engine block and usually commands a premium price when offered for sale.
The EN40B spec crankshaft was the original specification as the original 1275cc Midget/Sprite engine was built to virtually the same specification as the Cooper S but made for an inline installation.
The EN40B crankshaft was Nitrided and if reground more than 0.010" needs to be re-treated.
The original specification conrods were also the same as the Cooper S EN24V - forging numbers AEG177 or AEG521.
The rods were later reduced to EN21 spec but more than adequate for normal use.
A nice set of AEG177 rods currently on 'e' bay
http://www.ebay.co.uk/itm/Set-Original- ... SwHMJYLIOo
The counterbore is the narrowest tube section in the rear of the crankshaft which you call the pocket.
Regarding the gearbox - as Richard says - before you do anything re stripping the box check the Pt Number (22G229) stamped on the first motion shaft just to the rear of the splines.